iMeta最新文献

{"title":"SIDERITE: Unveiling hidden siderophore diversity in the chemical space through digital exploration","authors":"Ruolin He,&nbsp;Shaohua Gu,&nbsp;Jiazheng Xu,&nbsp;Xuejian Li,&nbsp;Haoran Chen,&nbsp;Zhengying Shao,&nbsp;Fanhao Wang,&nbsp;Jiqi Shao,&nbsp;Wen-Bing Yin,&nbsp;Long Qian,&nbsp;Zhong Wei,&nbsp;Zhiyuan Li","doi":"10.1002/imt2.192","DOIUrl":"https://doi.org/10.1002/imt2.192","url":null,"abstract":"<p>In this work, we introduced a siderophore information database (SIDERTE), a digitized siderophore information database containing 649 unique structures. Leveraging this digitalized data set, we gained a systematic overview of siderophores by their clustering patterns in the chemical space. Building upon this, we developed a functional group-based method for predicting new iron-binding molecules with experimental validation. Expanding our approach to the collection of open natural products (COCONUT) database, we predicted a staggering 3199 siderophore candidates, showcasing remarkable structure diversity that is largely unexplored. Our study provides a valuable resource for accelerating the discovery of novel iron-binding molecules and advancing our understanding of siderophores.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.192","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete telomere-to-telomere assemblies of two sorghum genomes to guide biological discovery","authors":"Chuanzheng Wei,&nbsp;Lei Gao,&nbsp;Ruixue Xiao,&nbsp;Yanbo Wang,&nbsp;Bingru Chen,&nbsp;Wenhui Zou,&nbsp;Jihong Li,&nbsp;Emma Mace,&nbsp;David Jordan,&nbsp;Yongfu Tao","doi":"10.1002/imt2.193","DOIUrl":"https://doi.org/10.1002/imt2.193","url":null,"abstract":"<p>The assembly of two sorghum T2T genomes corrected the assembly errors in the current reference, uncovered centromere variation, boosted functional genomics research, and accelerated sorghum improvement.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.193","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SeqKit2: A Swiss army knife for sequence and alignment processing","authors":"Wei Shen,&nbsp;Botond Sipos,&nbsp;Liuyang Zhao","doi":"10.1002/imt2.191","DOIUrl":"10.1002/imt2.191","url":null,"abstract":"<p>In the era of ubiquitous high-throughput sequencing studies, there is a growing need for analysis tools that are not just performant but also comprehensive and user-friendly enough to cater to both novice and advanced users. This article introduces SeqKit2, the next iteration of the widely used sequence analysis tool SeqKit, featuring expanded functionality, performance optimizations, and support for additional compression methods. Retaining a pragmatic subcommand architecture, SeqKit2 represents substantial enhancement through the inclusion of 19 additional subcommands, expanding its overall repertoire to a total of 38 in eight categories. The new subcommands add functionality such as amplicon processing and robust, error-tolerant parsing of sequence records. In addition, three subcommands designed for real-time analysis are added for periodic monitoring of properties of FASTQ and Binary Alignment/Map alignment records and real-time streaming from multiple sequence files. The performance of SeqKit2 is benchmarked against the old version of SeqKit, Bioawk, Seqtk, and SeqFu tools. SeqKit2 consistently outperforms its predecessor, albeit with marginally higher memory usage, while maintaining competitive runtimes against other tools. With its broad functionality, proven usability, and ongoing development driven by user feedback, we hope that bioinformaticians will find SeqKit2 useful as a “Swiss army knife” of sequence and alignment processing—equally adept at facilitating ad hoc analyses and seamlessly integrating into larger pipelines.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.191","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140737038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome-mediated alleviation of tobacco replant problem via autotoxin degradation after long-term continuous cropping","authors":"Peixue Xuan,&nbsp;Haikun Ma,&nbsp;Xiaopeng Deng,&nbsp;Yunfu Li,&nbsp;Jianqing Tian,&nbsp;Junying Li,&nbsp;Erdeng Ma,&nbsp;Zhaoli Xu,&nbsp;Dong Xiao,&nbsp;T. Martijn Bezemer,&nbsp;Mingfeng Wang,&nbsp;Xingzhong Liu,&nbsp;Meichun Xiang","doi":"10.1002/imt2.189","DOIUrl":"https://doi.org/10.1002/imt2.189","url":null,"abstract":"<p>Continuous cropping often results in severe “replant problem,” across various crops due to the autotoxins accumulation, soil acidification, pathogens proliferation, and microbial dysfunction. We unveiled a groundbreaking phenomenon that long-term continuous cropping (LTCC) can alleviate the tobacco replant problem. This mitigation occurs through the enrichment of autotoxin-degrading microbes, and the transformative impact is evident with even a modest application (10%) of LTCC soil to short-term continuous cropping (STCC) soil. Our investigation has pinpointed specific autotoxin-degrading bacteria, particularly the <i>Pseudomonas</i> and <i>Burkholderia</i> species, which exhibit the capacity to alleviate the tobacco replant problem in STCC soil. Their autotoxin-degrading mechanism using axenic culture and soil samples was also conducted via comprehensive analyses of microbiome and transcriptome approach. This research sheds light on the potential of LTCC as a strategic approach for sustainable agriculture, addressing replant problems and promoting the health of cropping systems. UV, ultraviolet; OD, optical density.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.189","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling interindividual variation of trimethylamine N-oxide and its precursors at the population level","authors":"Sergio Andreu-Sánchez,&nbsp;Shahzad Ahmad,&nbsp;Alexander Kurilshikov,&nbsp;Marian Beekman,&nbsp;Mohsen Ghanbari,&nbsp;Martijn van Faassen,&nbsp;Inge C. L. van den Munckhof,&nbsp;Marinka Steur,&nbsp;Amy Harms,&nbsp;Thomas Hankemeier,&nbsp;M. Arfan Ikram,&nbsp;Maryam Kavousi,&nbsp;Trudy Voortman,&nbsp;Robert Kraaij,&nbsp;Mihai G. Netea,&nbsp;Joost H. W. Rutten,&nbsp;Niels P. Riksen,&nbsp;Alexandra Zhernakova,&nbsp;Folkert Kuipers,&nbsp;P. Eline Slagboom,&nbsp;Cornelia M. van Duijn,&nbsp;Jingyuan Fu,&nbsp;Dina Vojinovic","doi":"10.1002/imt2.183","DOIUrl":"10.1002/imt2.183","url":null,"abstract":"<p>Trimethylamine <i>N</i>-oxide (TMAO) is a circulating microbiome-derived metabolite implicated in the development of atherosclerosis and cardiovascular disease (CVD). We investigated whether plasma levels of TMAO, its precursors (betaine, carnitine, deoxycarnitine, choline), and TMAO-to-precursor ratios are associated with clinical outcomes, including CVD and mortality. This was followed by an in-depth analysis of their genetic, gut microbial, and dietary determinants. The analyses were conducted in five Dutch prospective cohort studies including 7834 individuals. To further investigate association results, Mendelian Randomization (MR) was also explored. We found only plasma choline levels (hazard ratio [HR] 1.17, [95% CI 1.07; 1.28]) and not TMAO to be associated with CVD risk. Our association analyses uncovered 10 genome-wide significant loci, including novel genomic regions for betaine (6p21.1, 6q25.3), choline (2q34, 5q31.1), and deoxycarnitine (10q21.2, 11p14.2) comprising several metabolic gene associations, for example, <i>CPS1</i> or <i>PEMT</i>. Furthermore, our analyses uncovered 68 gut microbiota associations, mainly related to TMAO-to-precursors ratios and the Ruminococcaceae family, and 16 associations of food groups and metabolites including fish-TMAO, meat-carnitine, and plant-based food-betaine associations. No significant association was identified by the MR approach. Our analyses provide novel insights into the TMAO pathway, its determinants, and pathophysiological impact on the general population.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.183","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140364255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches","authors":"Jiayu Zhang,&nbsp;Aixi Tang,&nbsp;Tao Jin,&nbsp;Deshou Sun,&nbsp;Fangliang Guo,&nbsp;Huaxin Lei,&nbsp;Lin Lin,&nbsp;Wensheng Shu,&nbsp;Pingfeng Yu,&nbsp;Xiaoyan Li,&nbsp;Bing Li","doi":"10.1002/imt2.188","DOIUrl":"10.1002/imt2.188","url":null,"abstract":"<p>Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.188","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140366829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactobacillus rhamnosus GG triggers intestinal epithelium injury in zebrafish revealing host dependent beneficial effects","authors":"Zhen Zhang,&nbsp;Hong-Ling Zhang,&nbsp;Da-Hai Yang,&nbsp;Qiang Hao,&nbsp;Hong-Wei Yang,&nbsp;De-Long Meng,&nbsp;Willem Meindert de Vos,&nbsp;Le-Luo Guan,&nbsp;Shu-Bin Liu,&nbsp;Tsegay Teame,&nbsp;Chen-Chen Gao,&nbsp;Chao Ran,&nbsp;Ya-Lin Yang,&nbsp;Yuan-Yuan Yao,&nbsp;Qian-Wen Ding,&nbsp;Zhi-Gang Zhou","doi":"10.1002/imt2.181","DOIUrl":"10.1002/imt2.181","url":null,"abstract":"<p><i>Lactobacillus rhamnosus</i> GG (LGG), the well-characterized human-derived probiotic strain, possesses excellent properties in the maintenance of intestinal homeostasis, immunoregulation and defense against gastrointestinal pathogens in mammals. Here, we demonstrate that the SpaC pilin of LGG causes intestinal epithelium injury by inducing cell pyroptosis and gut microbial dysbiosis in zebrafish. Dietary SpaC activates Caspase-3−GSDMEa pathways in the intestinal epithelium, promotes intestinal pyroptosis and increases lipopolysaccharide (LPS)-producing gut microbes in zebrafish. The increased LPS subsequently activates Gaspy2−GSDMEb pyroptosis pathway. Further analysis reveals the Caspase-3−GSDMEa pyroptosis is initiated by the species-specific recognition of SpaC by TLR4ba, which accounts for the species-specificity of the SpaC-inducing intestinal pyroptosis in zebrafish. The observed pyroptosis-driven gut injury and microbial dysbiosis by LGG in zebrafish suggest that host-specific beneficial/harmful mechanisms are critical safety issues when applying probiotics derived from other host species and need more attention.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140383030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arbuscular mycorrhizal fungal interactions bridge the support of root-associated microbiota for slope multifunctionality in an erosion-prone ecosystem","authors":"Tianyi Qiu,&nbsp;Josep Peñuelas,&nbsp;Yinglong Chen,&nbsp;Jordi Sardans,&nbsp;Jialuo Yu,&nbsp;Zhiyuan Xu,&nbsp;Qingliang Cui,&nbsp;Ji Liu,&nbsp;Yongxing Cui,&nbsp;Shuling Zhao,&nbsp;Jing Chen,&nbsp;Yunqiang Wang,&nbsp;Linchuan Fang","doi":"10.1002/imt2.187","DOIUrl":"10.1002/imt2.187","url":null,"abstract":"<p>The role of diverse soil microbiota in restoring erosion-induced degraded lands is well recognized. Yet, the facilitative interactions among symbiotic arbuscular mycorrhizal (AM) fungi, rhizobia, and heterotrophic bacteria, which underpin multiple functions in eroded ecosystems, remain unclear. Here, we utilized quantitative microbiota profiling and ecological network analyses to explore the interplay between the diversity and biotic associations of root-associated microbiota and multifunctionality across an eroded slope of a <i>Robinia pseudoacacia</i> plantation on the Loess Plateau. We found explicit variations in slope multifunctionality across different slope positions, associated with shifts in limiting resources, including soil phosphorus (P) and moisture. To cope with P limitation, AM fungi were recruited by <i>R. pseudoacacia</i>, assuming pivotal roles as keystones and connectors within cross-kingdom networks. Furthermore, AM fungi facilitated the assembly and composition of bacterial and rhizobial communities, collectively driving slope multifunctionality. The symbiotic association among <i>R. pseudoacacia</i>, AM fungi, and rhizobia promoted slope multifunctionality through enhanced decomposition of recalcitrant compounds, improved P mineralization potential, and optimized microbial metabolism. Overall, our findings highlight the crucial role of AM fungal-centered microbiota associated with <i>R. pseudoacacia</i> in functional delivery within eroded landscapes, providing valuable insights for the sustainable restoration of degraded ecosystems in erosion-prone regions.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.187","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140384789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Microbiome Protocols eBook initiative: Building a bridge to microbiome research","authors":"Yunyun Gao,&nbsp;Kai Peng,&nbsp;Defeng Bai,&nbsp;Xiao-Ye Bai,&nbsp;Yujing Bi,&nbsp;Anqi Chen,&nbsp;Baodong Chen,&nbsp;Feng Chen,&nbsp;Juan Chen,&nbsp;Lei Chen,&nbsp;Tong Chen,&nbsp;Wei Chen,&nbsp;Xu Cheng,&nbsp;Yanfen Cheng,&nbsp;Jie Cui,&nbsp;Jingjing Dai,&nbsp;Junbiao Dai,&nbsp;Zhaolai Dai,&nbsp;Ye Deng,&nbsp;Yi-Zhen Deng,&nbsp;Wei Ding,&nbsp;Zhencheng Fang,&nbsp;Wei Fu,&nbsp;Hanbing Gao,&nbsp;Shaohua Gu,&nbsp;Xue Guo,&nbsp;Xuguang Guo,&nbsp;Dongfei Han,&nbsp;Lele He,&nbsp;Yatao He,&nbsp;Hui-Yu Hou,&nbsp;Baolei Jia,&nbsp;Gengjie Jia,&nbsp;Shuo Jiao,&nbsp;Wei Jin,&nbsp;Feng Ju,&nbsp;Zhicheng Ju,&nbsp;Siyuan Kong,&nbsp;Canhui Lan,&nbsp;Bing Li,&nbsp;Da Li,&nbsp;Diyan Li,&nbsp;Jingdi Li,&nbsp;Meng Li,&nbsp;Qi Li,&nbsp;Qiang Li,&nbsp;Wen-Jun Li,&nbsp;Xiaofang Li,&nbsp;Xuemeng Li,&nbsp;Yahui Li,&nbsp;You-Gui Li,&nbsp;Zhibin Liang,&nbsp;Ning Ling,&nbsp;Fufeng Liu,&nbsp;Qing Liu,&nbsp;Shuang-Jiang Liu,&nbsp;Hongye Lu,&nbsp;Qi Lu,&nbsp;Guangwen Luo,&nbsp;Hao Luo,&nbsp;Yuheng Luo,&nbsp;Hujie Lyu,&nbsp;Chuang Ma,&nbsp;Liyuan Ma,&nbsp;Tengfei Ma,&nbsp;Jinfeng Ni,&nbsp;Ziqin Pang,&nbsp;Xiaojing Qiang,&nbsp;Yuan Qin,&nbsp;Qingyue Qu,&nbsp;Chao Ran,&nbsp;Shuqiang Ren,&nbsp;Haitao Shang,&nbsp;Luyang Song,&nbsp;Linyang Sun,&nbsp;Weimin Sun,&nbsp;Liping Tang,&nbsp;Jian Tian,&nbsp;Kai Wang,&nbsp;Mengzhi Wang,&nbsp;Ming-Ke Wang,&nbsp;Tao Wang,&nbsp;Xiao-Yan Wang,&nbsp;Yao Wang,&nbsp;Yiwen Wang,&nbsp;Youshan Wang,&nbsp;Hailei Wei,&nbsp;Hong Wei,&nbsp;Zhong Wei,&nbsp;Tao Wen,&nbsp;Jiqiu Wu,&nbsp;Linhuan Wu,&nbsp;Linkun Wu,&nbsp;Jiao Xi,&nbsp;Bo Xie,&nbsp;Guofang Xu,&nbsp;Jun Xu,&nbsp;Shanshan Xu,&nbsp;Qing Xue,&nbsp;Liping Yan,&nbsp;Haifei Yang,&nbsp;Jun Yang,&nbsp;Junbo Yang,&nbsp;Ruifu Yang,&nbsp;Yalin Yang,&nbsp;Ying-Jie Yang,&nbsp;Xiaofang Yao,&nbsp;Yanpo Yao,&nbsp;Salsabeel Yousuf,&nbsp;Ke Yu,&nbsp;Zhengrong Yuan,&nbsp;Zhilin Yuan,&nbsp;Dong Zhang,&nbsp;Tianyuan Zhang,&nbsp;Weipeng Zhang,&nbsp;Yunzeng Zhang,&nbsp;Zhaonan Zhang,&nbsp;Zhen Zhang,&nbsp;Zhi-Feng Zhang,&nbsp;Shengguo Zhao,&nbsp;Wei Zhao,&nbsp;Maosheng Zheng,&nbsp;Ziqiang Zheng,&nbsp;Xin Zhou,&nbsp;Yuanping Zhou,&nbsp;Zhigang Zhou,&nbsp;Mo Zhu,&nbsp;Yong-Guan Zhu,&nbsp;Haiyan Chu,&nbsp;Yang Bai,&nbsp;Yong-Xin Liu","doi":"10.1002/imt2.182","DOIUrl":"10.1002/imt2.182","url":null,"abstract":"<p>The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.182","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140230976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects","authors":"Ji-Hong Liu,&nbsp;Yizhou Zhang,&nbsp;Ning Zhou,&nbsp;Jiale He,&nbsp;Jing Xu,&nbsp;Zhao Cai,&nbsp;Liang Yang,&nbsp;Yang Liu","doi":"10.1002/imt2.186","DOIUrl":"10.1002/imt2.186","url":null,"abstract":"<p>DNA methylation serves as the primary mode of epigenetic regulation in prokaryotes, particularly through transcriptional regulation. With the rapid implementation of third-generation sequencing technology, we are currently experiencing a golden age of bacterial epigenomics. However, there has been a lack of comprehensive research exploring the versatility and consequential impact of bacterial DNA methylome on cellular and physiological functions. There is a critical need for a user-friendly bioinformatics tool that can effectively characterize DNA methylation modification features and predict the regulation patterns. To address this gap, the current study introduces Bacmethy, an innovative tool that utilizes SMRT-seq data and offers a range of analytical modules. First, the tool classifies methylation sites in the genome, highlighting the distinct regulations present under varying modification fractions and location enrichment. Furthermore, this tool enables us to identify regulatory region methylation and potential <i>cis</i> and <i>trans</i> interactions between methylation sites and regulatory effectors. Using benchmark data sets and our data, we show that our tool facilitates the understanding of the distinctive traits of DNA methylation modifications and predicts transcriptional regulation effects on important physiological and pathological functions. Bacmethy code is freely available, and the Docker image is downloadable. Bacmethy has been made available as a user-friendly web server interface at https://bacmethy.med.sustech.edu.cn.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.186","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140230450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}